Structure and activity of spontaneous fungal communities in organic substrates used for soilless crops

•Microbial activity of organic growing media was evaluated.•Microbial structure and activity is specific of the organic growing media.•Cellulose to lignin ratio is not relevant to predict microbial structure and activity.

Microbiological activity in substrates is of considerable concern for stability of the material and control of plant pathogens in the root environment. This study analyzes the structure of spontaneous microbial communities in various organic substrates used for soilless crops. Different wood fibers, coir fibers and peats were incubated in controlled conditions. The activity of indigenous microorganisms was monitored by assessing substrate mineralization (CO2 released by substrates, potential enzymatic activity and lignocellulosic composition). The genetic structure of the fungal communities was analyzed by PCR-TTGE. Behavior was repeatable across different batches. Potential enzymatic activity was poorly correlated to microbial respiration and lignocellulosic composition. Microbial structure was specific to each substrate. The highest microbial specificity was for wood fibers, then coir fibers, and finally peats. Our data indicated that microbial activity strongly depends on substrate origin and manufacturing process. Our results suggest that spontaneous development of microorganisms within a substrate could have specific effects on organic matter evolution and disease control.